Motor-protein "roundabouts": microtubules moving on kinesin-coated tracks through engineered networks

Nanotechnology promises to enhance the functionality and sensitivity of miniaturized analytical systems. For example, nanoscale transport systems, which are driven by molecular motors, permit the controlled movement of select cargo along predetermined paths. Such shuttle systems may enhance the detection efficiency of an analytical system or facilitate the controlled assembly of sophisticated nanostructures if transport can be coordinated through complex track networks. This study determines the feasibility of complex track networks using kinesin motor proteins to actively transport microtubule shuttles along micropatterned surfaces. In particular, we describe the performance of three basic structural motifs: (1) crossing junctions, (2) directional sorters, and (3) concentrators. We also designed track networks that successfully sort and collect microtubule shuttles, pointing the way towards lab-on-a-chip devices powered by active transport instead of pressure-driven or electroosmotic flow.     

Mechanical properties of single motor molecules studied by three-dimensional thermal force probing in optical tweezers.

A new method combining three-dimensional (3D) force measurements in an optical trap with the analysis of thermally induced (Brownian) position fluctuations of a trapped probe was used to investigate the mechanical properties of a single molecule, the molecular motor kinesin. One kinesin molecule attached to the probe was bound in a rigorlike state to one microtubule. The optical trap was kept weak to measure the thermal forces acting on the probe, which were mainly counterbalanced by the kinesin tether. The stiffness of kinesin during stretching and compression with respect to its backbone axis were measured. Our results indicate that a section of kinesin close to the motor domain is the dominating element in the flexibility of the motor structure. The experiments demonstrate the power of 3D thermal fluctuation analysis to characterize mechanical properties of individual motor proteins and indicate its usefulness to study single molecule in general     

Kinesin superfamily protein member 4 (KIF4) is localized to midzone and midbody in dividing cells

In association with microtubules, a variety of kinesins play important roles in cellular functions such as intracellular transport of organelles or vesicles, signal transduction, and cell division. In a previous study we revealed that human kinesin superfamily protein member 4 (KIF4) is a chromokinesin that binds to chromosomes. Since localization of several kinds of kinesin at midzone called central spindle, or midbody that connects two daughter cells, or both, suggests their implication in cell division, we investigated KIF4 localization of during mitosis and cytokinesis in Hela cells. In addition to association with segregating chromosomes through entire mitosis, it also localized to the midzone and to midbody at ana/telophase through cytokinesis. Especially in cells at cytokinesis, KIF4 appeared as a doublet facing each other at the apical ends of two daughter cells. Three- dimensional analysis of architectural relationship between microtubule bundles and KIF4 indicated that KIF4 forms a ring structure wrapping around the microtubule bundles. These results suggest that KIF4 is involved in cytokinesis, although direct evidence was not provided in this study.     

Quantum chemical analysis of electronic structure and n- and p-type charge transport in perfluoroarene-modified oligothiophene semiconductors

Density-functional theory (DFT) is employed to investigate the structural, electronic, and transport properties of several isomeric fluoroarene-oligothiophene-based semiconductors. Three oligothiophene systems varying in the perfluoroarene group positions within the molecule are studied to understand the electronic structure leading to the observed mobility values and to the n- or p-type behavior in these structures. Analyses of both intermolecular interactions in dimers and extended interactions in crystalline structures afford considerable insight into the electronic properties and carrier mobilities of these materials, as well as the polarity of the charge carriers. From the calculated carrier effective masses, we find that sterically governed molecular planarity plays a crucial role in the transport properties of these semiconductors. Our calculations correlate well with experimentally obtained geometries, highest-occupied molecular orbital (HOMO)/lowest-unoccupied molecular orbital (LUMO) energies, and the experimental carrier mobility trends among the systems investigated.     

Controlled Retention and Release of Biomolecular Transport Systems Using Shape‐Changing Polymer Bilayers

Biomolecular transport systems based on cytoskeletal filaments and motor proteins have become promising tools for a wide range of nanotechnological applications. In this paper, we report control of such transport systems using substrates with switchable shape. We demonstrate this approach on the example of microtubules gliding on surfaces of self‐folding polymer bilayers with adsorbed kinesin motors. The polymer bilayers are able to undergo reversible transitions between flat and tube‐like shapes that allow the externally controlled retention and release of gliding microtubules. The demonstrated approach, based on surfaces with reconfigurable topography, opens broad perspectives to control biomolecular transport systems for bioanalytical and sensing applications, as well as for the construction of subcellular compartments in the field of synthetic biology.     

Dynamic photo-control of kinesin on a photoisomerizable monolayer--hydrolysis rate of ATP and motility of microtubules depending on the terminal group

The reversibly and repeatedly altered gliding motility of microtubules driven by kinesin on the photoresponsive monolayer surface is studied. It was confirmed that an azobenzene monolayer surface needs to have free amino terminal groups for the successful dynamic control of the motility of microtubule. The surface of the azobenzene monolayer with terminal amino groups can dynamically control the ATP hydrolysis activity of kinesin which resulted in the change in motility of the microtubules.     

Microtubule dynamics regulated by stathmin

Microtubules perform a variety of functions which lead to the complex regulation of intracellular transport and cell division. However, the regulation of microtubule growth is not clearly known. Based on a recent experimental finding, we explore the possibility of spatial regulation of microtubule growth by stathmin–tubulin interaction gradients. Computer simulation of the model with stathmin–tubulin interaction gradients gave regulated growth as seen in experiments. In future, the stathmin–tubulin interaction gradients can be made dynamic and its impact on the microtubule growth can be explored.     

Prediction of Vapor–Liquid Equilibria for Pb–Pd and Pb–Pt Alloys Using Ab Initio Methods in Vacuum Distillation

The vapor–liquid equilibrium (VLE) phase diagrams of Pb–Pd and Pb–Pt alloy systems in vacuum distillation were obtained based only on pure-component properties and the structures of the atoms. The interaction energies between pairs of atoms were calculated from ab initio methods and were used as the input energy parameters for the Wilson equation. The calculated activity data of the components, using energy parameters which were obtained by ab initio methods, are in good agreement with the experimental data. It is revealed that a cluster size of eight atoms, optimized using the NVT ensemble at 300 K, a time step of 1 femtosecond, and the simulation time 10 ps gives a good representation of the liquid phase systems. This approach can be used to obtain accurate VLE predictions for alloy systems in vacuum distillation. The VLE phase diagram has a significant advantage in guiding experiment and industrial production in vacuum metallurgy.     

Transport parameters of glassy polymers: Effect of occupied and accessible volumes

The occupied and accessible volumes have been calculated for 32 polyimides of various structures. The calculation data have been compared with the experimentally measured transport parameters for one polymer-various gases and one gas-various polymers systems. The correlation coefficients have been estimated as 90–98%. The transport parameters plotted as a function of the Kuhn segment are described by curves with maxima. The best transport characteristics are exhibited by polymers with Kuhn segment lengths of 60–80 Å.     

Setting up roadblocks for kinesin-1: mechanism for the selective speed control of cargo carrying microtubules

Motor-driven cytoskeletal filaments are versatile transport platforms for nanosized cargo in molecular sorting and nano-assembly devices. However, because cargo and motors share the filament lattice as a common substrate for their activity, it is important to understand the influence of cargo-loading on transport properties. By performing single-molecule stepping assays on biotinylated microtubules we found that individual kinesin-1 motors frequently stopped upon encounters with attached streptavidin molecules. Consequently, we attribute the deceleration of cargo-laden microtubules in gliding assays to an obstruction of kinesin-1 paths on the microtubule lattice rather than to 'frictional' cargo-surface interactions. We propose to apply this obstacle-caused slow-down of gliding microtubules in a novel molecular detection scheme: Using a mixture of two distinct microtubule populations that each bind a different kind of protein, the presence of these proteins can be detected via speed changes in the respective microtubule populations.     

Observation of individual microtubule motor steps in living cells with endocytosed quantum dots

We report the observation of individual steps taken by motor proteins in living cells by following movements of endocytic vesicles that contain quantum dots (QDs) with a fast camera. The brightness and photostability of quantum dots allow us to record motor displacement traces with 300 micros time resolution and 1.5 nm spatial precision. We observed individual 8 nm steps in active transport toward both the microtubule plus- and minus-ends, the directions of kinesin and dynein movements, respectively. In addition, we clearly resolved abrupt 16 nm steps in the plus-end direction and often consecutive 16 nm and occasional 24 nm steps in minus-end directed movements. This work demonstrates the ability of the QD assay to probe the operation of motor proteins at the molecular level in living cells under physiological conditions.     

A synthetic DNA walker for molecular transport

Inspired by kinesin movement along a microtubule, we demonstrate a processive bipedal DNA walker. Powered by externally controlled DNA fuel strands, the walker locomotes with a 5 nm stride by advancing the trailing foot to the lead at each step. Real-time monitoring of specific bidirectional walker movement is achieved via multiplexed fluorescence quenching.     

A first-principles description of liquid BeF2 and its mixtures with LiF: 2. Network formation in LiF-BeF2

A polarizable ionic interaction potential, constructed from first-principles calculations, is used to examine the structure, vibrational spectra, and transport properties of molten mixtures of LiF and BeF2 across a range of compositions. The simulations reproduce the experimentally measured vibrational frequencies of the fluoroberyllate (BeF4(2-)) ions, which form in the melt, as well as conductivity and viscosity values across the composition range. Examination of the structures of the melts reveals the emergence of a slowly relaxing network of BeF4 units as the concentration of BeF2 is increased. The relationship between the appearance of the network and the composition dependence of the transport properties is explored.     

Coarse-graining kinetic networks in photosynthetic energy transport

Photosynthetic systems utilize hundreds of chlorophylls to collect sunlight and transport the energy to the reaction center with remarkably high quantum efficiency, however, the large size of the system together with the complex interactions among the components make it extremely challenging to understand the dynamics of light harvesting in large photosynthetic systems. To shed light on this problem, we present a structure-based theoretical framework that can be used to calculate transition rate matrix describing energy transport in photosynthetic systems and network clustering methods that provide simplified coarse-grained model revealing key structures guiding the light harvesting process. We constructed an effective model for energy transport in a Photosystem II supercomplex and applied several network clustering methods to generate coarse-grained kinetic cluster models for the system. Furthermore, we evaluated the performances of the network clustering methods, and show that a spectral clustering method and a minimum cut approach produce accurate coarse-grained models for the PSII-sc system. The results indicate that finding bottlenecks of energy transport is a crucial factor for reduced representations of photosynthetic light harvesting, and the overall work presented in this paper should provide a comprehensive theoretical framework to elucidate the dynamics of light harvesting in photosynthetic systems.     

Walking molecules

Movement is intrinsic to life. Biologists have established that most forms of directed nanoscopic, microscopic and, ultimately, macroscopic movements are powered by molecular motors from the dynein, myosin and kinesin superfamilies. These motor proteins literally walk, step by step, along polymeric filaments, carrying out essential tasks such as organelle transport. In the last few years biological molecular walkers have inspired the development of artificial systems that mimic aspects of their dynamics. Several DNA-based molecular walkers have been synthesised and shown to walk directionally along a track upon sequential addition of appropriate chemical fuels. In other studies, autonomous operation--i.e. DNA-walker migration that continues as long as a complex DNA fuel is present--has been demonstrated and sophisticated tasks performed, such as moving gold nanoparticles from place-to-place and assistance in sequential chemical synthesis. Small-molecule systems, an order of magnitude smaller in each dimension and 1000× smaller in molecular weight than biological motor proteins or the walker systems constructed from DNA, have also been designed and operated such that molecular fragments can be progressively transported directionally along short molecular tracks. The small-molecule systems can be powered by light or chemical fuels. In this critical review the biological motor proteins from the kinesin, myosin and dynein families are analysed as systems from which the designers of synthetic systems can learn, ratchet concepts for transporting Brownian substrates are discussed as the mechanisms by which molecular motors need to operate, and the progress made with synthetic DNA and small-molecule walker systems reviewed (142 references).     

Structures and electronic transport on silicon surfaces

By utilizing a variety of surface superstructures formed on silicon surfaces and atomic layers grown on them, close correlations between the atomic-scale structures and electrical conduction phenomena at the surfaces have been revealed. State-of-art techniques for analyzing and controlling atomic/electronic structures of surfaces are leading to an understanding of the novel electronic transport properties at surfaces. For example, the electrical conduction through surface-state bands, which are inherent in the surface superstructure, has been confirmed in in-situ measurements. An important phenomenon has also been found, where adatoms donate carriers into the surface-state band, resulting in a remarkable enhancement in electrical conductance. The nucleation of the adatoms diminishes such a doping effect. Furthermore, electrical conduction through atomic layers grown on the surfaces, whose growth structures are sensitive to the substrate surface structures, will be also discussed. In this review, we emphasize that the surface electronic transport properties are closely related to the atomic structures and atomistic dynamics on surfaces. The ultimate two-dimensional electron systems, consisting of the surface-state bands and grown atomic layers, are expected to provide a new stage in surface physics, as well as a precursory stage leading to atomic-scale electronics devices.     

A model for the creep of oriented high-modulus fibers

Recently it has been shown that the creep of oriented high-modulus fibers satisfies a logarithmic time law over very long time intervals. Moreover, the modulus of these fibers increases due to the creep. This was interpreted by the annihilation of conformation defects during creep. In structures with strong intermolecular interactions as in aramides, however, the direct annihilation of defects is difficult to explain. Moreover a direct annihilation leads to a false time law if no further assumption about the properties of the defects are made. In this paper a model for the transport of conformation defects in oriented polymer chains imbedded into an oriented fibrillary structure with strong intermolecular interactions is presented. This modified transport model leads directly to the experimentally observed time law without any further assumptions about the defect properties.     

3,5,7,9-Substituted hexaazaacridines: toward structures with nearly degenerate singlet-triplet energy separations

Toward the goal of preparing stable, neutral open-shell systems, we synthesized a novel series of p-phenyl-substituted 3,5,7,9-hexaazaacridine and 3,5,7,9-hexaazaanthracene derivatives. The effects of substitution on the molecular electronic properties were probed both experimentally and computationally [B3LYP/6-311G(d,p)//B3LYP/6-31G(d,p)]. While the experimentally prepared structures already have small (20-25 kcal/mol) singlet-triplet energy gaps, systems with even smaller (<9 kcal/mol) singlet-triplet energy separations can be realized through systematic variation of the substituent numbers, types, and patterns. Hexaazaanthracenes show generally smaller singlet-triplet energy gaps than hexaazaacridines. Nitrogen-bonded sigma- and pi-acceptor substituents that cause positive inductive and mesomeric effects as well as carbon-bonded sigma-donor substituents make substituted hexaazaanthracenes promising candidates for purely organic high-spin systems.     

Influence of Intermolecular N?H⋅⋅⋅π Interactions on Molecular Packing and Field‐Effect Performance of Organic Semiconductors

Charge transport in organic semiconductors is strongly dependent on their molecular packing modes in the solid state. Therefore, understanding the relationship between molecular packing and charge transport is imperative, both experimentally and theoretically. However, so far, the fundamental effects of solid‐state packing and molecular interactions (e.g. N? H ??? π) on charge transport need further elucidation. Herein, indolo[3,2‐b]carbazole (ICZ) and a derivative thereof are used as examples to approach this scientific target. An interesting insight obtained thereby is that N? H ??? π interactions among ICZ molecules facilitate charge transport for higher mobility. Subtle changes in the of N? H ??? π interactions can significantly influence both the molecular packing and the charge‐transport properties. Therefore, a method for exploiting intermolecular N? H ??? π interactions would yield novel molecular systems with designable characteristics.